Pseudotime reconstruction using TSCAN

Zhicheng Ji, Hongkai Ji

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Scopus citations


In many single-cell RNA-seq (scRNA-seq) experiments, cells represent progressively changing states along a continuous biological process. A useful approach to analyzing data from such experiments is to computationally order cells based on their gradual transition of gene expression. The ordered cells can be viewed as samples drawn from a pseudo-temporal trajectory. Analyzing gene expression dynamics along the pseudotime provides a valuable tool for reconstructing the underlying biological process and generating biological insights. TSCAN is an R package to support in silico reconstruction of cells’ pseudotime. This chapter introduces how to apply TSCAN to scRNA-seq data to perform pseudotime analysis.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages10
StatePublished - 2019

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745


  • Bioinformatics
  • Gene expression
  • Genomics
  • Minimum spanning tree
  • Pseudotime
  • Single-cell RNA-seq

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


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